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Cython Implementation of Orthogonal Matching Pursuit

This repository implements orthogonal matching pursuit (OMP) and least absolute shrinkage and selection operator (lasso) algorithm in numba and Cython.

Requirements

Install the requirements:

sudo apt-get install libatlas-base-dev # or equivalent
pip install -r requirements.txt

Then add project and reconstruction methods directories to $PYTHONPATH:

export PYTHONPATH="${PYTHONPATH}:/path/containing/project/directory/"
export PYTHONPATH="${PYTHONPATH}:/path/containing/project/directory/cython-omp/src/reconstruction_methods/" # this is because of ray's relative import inability

Following commands assume the name of the folder is cython-omp.

Dictionary Learning

To learn the overcomplete dictionary, run:

python -m cython-omp.src.learn_patch_dict

Compiling Cython scripts

cd src/reconstruction_methods
python omp_setup.py build_ext --inplace
python lasso_setup.py build_ext --inplace

Reconstruction Demo

python -m cython_omp.src.demo --method=<method>

choices for the method are:

  • OMP_numba
  • OMP_batch_numba
  • OMP_cython
  • OMP_batch_cython (default)
  • lasso_numba
  • lasso_batch_numba
  • lasso_cython
  • lasso_batch_cython

License

Apache License 2.0